How to caluculate buried surface area
Dear Chimera I am sorry to interrupt your busy schedule. My name is Matsui, and I am a second-year master's student at a Japanese university. Thank you for taking time out of your busy schedule to respond to my question the other day. We are investigating the buried surface area to see the magnitude of the interaction between protein and ligand. For this purpose, I calculated the solvent accessible area of the ligand. However, the value is 9955, which shows the entire surface area of the protein. What should I do? I am not in a hurry for answers , so I would appreciate a reply when you have the time. In this case, the ligand was in the binding pocket of the protein, so I would like to calculate the ligand's solvent contact area = buried surface area. I tried to check and tried , but it did not work. 1.See https://www.cgl.ucsf.edu/pipermail/chimera-users/2009-January/003521.html 2.Try to use measure blob using chimera X. Reference: https://www.cgl.ucsf.edu/chimerax/docs/user/commands/measure.html#buriedarea However, I didn't know how to solve this command. Command ;ui mousemode right "pick blobs Reference; https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/ui.html --------------------------------------------------------------------------- Kenji Matsui Graduate School of Tokyo University of Agriculture and Technology M2 2-24-16, Nakamachi, Koganei-shi, Tokyo 184-8588, Japan
Hi Kenji, You are using ChimeraX? I CC'd the ChimeraX address chimerax-users@cgl.ucsf.edu (different than chimera-users@cgl.ucsf.edu). The "measure buriedArea" command does not require picking any blobs. You just specify the parts that you want in the command line. <https://www.cgl.ucsf.edu/chimerax/docs/user/commands/measure.html#buriedarea> So, maybe something like command: measure buriedarea protein with ligand ...but maybe "ligand" doesn't get your ligand. You would have to use whatever kind of specification works for your ligand, e.g. if residue name is UNK, something like this instead: measure buriedarea protein with :UNK You sent a Pymol session... I don't use Pymol so I can't open that file, sorry. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 5, 2022, at 9:45 PM, Kenji MATSUI via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Dear Chimera
I am sorry to interrupt your busy schedule.
My name is Matsui, and I am a second-year master's student at a Japanese university. Thank you for taking time out of your busy schedule to respond to my question the other day.
We are investigating the buried surface area to see the magnitude of the interaction between protein and ligand.
For this purpose, I calculated the solvent accessible area of the ligand. However, the value is 9955, which shows the entire surface area of the protein.
What should I do? I am not in a hurry for answers , so I would appreciate a reply when you have the time.
In this case, the ligand was in the binding pocket of the protein, so I would like to calculate the ligand's solvent contact area = buried surface area.
I tried to check and tried , but it did not work.
1.See https://www.cgl.ucsf.edu/pipermail/chimera-users/2009-January/003521.html
2.Try to use measure blob using chimera X. Reference: https://www.cgl.ucsf.edu/chimerax/docs/user/commands/measure.html#buriedarea
However, I didn't know how to solve this command. Command ;ui mousemode right "pick blobs
Reference; https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/ui.html --------------------------------------------------------------------------- Kenji Matsui Graduate School of Tokyo University of Agriculture and Technology M2 2-24-16, Nakamachi, Koganei-shi, Tokyo 184-8588, Japan
<Buried_surface_area_LXRα_1UHL_24,25-epoxy_cholesterol (remove LXRβ_1P8D).pse>_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users
Dear Elane Thank you for your time and response. My name is Matsui, and I am a second-year master's student at a Japanese university. I am also using ChimeraX. But first I will try the method you showed me with chimera, and if it doesn't work, I will try it with chimeraX as well. --------------------------------------------------------------------------- Kenji Matsui Graduate School of Tokyo University of Agriculture and Technology M2 2-24-16, Nakamachi, Koganei-shi, Tokyo 184-8588, Japan Mail: s214903z@st.go.tuat.ac.jp 2022年9月6日(火) 23:30 Elaine Meng <meng@cgl.ucsf.edu>:
Hi Kenji, You are using ChimeraX? I CC'd the ChimeraX address chimerax-users@cgl.ucsf.edu (different than chimera-users@cgl.ucsf.edu).
The "measure buriedArea" command does not require picking any blobs. You just specify the parts that you want in the command line. < https://www.cgl.ucsf.edu/chimerax/docs/user/commands/measure.html#buriedarea
So, maybe something like command:
measure buriedarea protein with ligand
...but maybe "ligand" doesn't get your ligand. You would have to use whatever kind of specification works for your ligand, e.g. if residue name is UNK, something like this instead:
measure buriedarea protein with :UNK
You sent a Pymol session... I don't use Pymol so I can't open that file, sorry. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 5, 2022, at 9:45 PM, Kenji MATSUI via Chimera-users < chimera-users@cgl.ucsf.edu> wrote:
Dear Chimera
I am sorry to interrupt your busy schedule.
My name is Matsui, and I am a second-year master's student at a Japanese university. Thank you for taking time out of your busy schedule to respond to my question the other day.
We are investigating the buried surface area to see the magnitude of the interaction between protein and ligand.
For this purpose, I calculated the solvent accessible area of the ligand. However, the value is 9955, which shows the entire surface area of the protein.
What should I do? I am not in a hurry for answers , so I would appreciate a reply when you have the time.
In this case, the ligand was in the binding pocket of the protein, so I would like to calculate the ligand's solvent contact area = buried surface area.
I tried to check and tried , but it did not work.
1.See https://www.cgl.ucsf.edu/pipermail/chimera-users/2009-January/003521.html
2.Try to use measure blob using chimera X. Reference: https://www.cgl.ucsf.edu/chimerax/docs/user/commands/measure.html#buriedarea
However, I didn't know how to solve this command. Command ;ui mousemode right "pick blobs
Reference; https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/ui.html
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Kenji Matsui Graduate School of Tokyo University of Agriculture and Technology M2 2-24-16, Nakamachi, Koganei-shi, Tokyo 184-8588, Japan
<Buried_surface_area_LXRα_1UHL_24,25-epoxy_cholesterol (remove LXRβ_1P8D).pse>_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users
participants (2)
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Elaine Meng -
Kenji MATSUI